Research workbench
Structure of the soluble domain of lipooligosaccharide phosphoethanolamine transferase a from neisseria meningitidis - complex with zn
Analyse Structure of the soluble domain of lipooligosaccharide phosphoethanolamine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KAY
- Type
- protein
- Length
- 666 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- YHBX/YHJW/YIJP/YJDB family protein
- EC
- 3.1.3.27
- UniProt
- Q7DD94
- Ligands
- ZN, PO4
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | YHBX/YHJW/YIJP/YJDB family protein (EC 3.1.3.27) | protein | 333 | 39% helix, 18% strand | Q7DD94 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.82 | 0.84 | 127 | ZN |
| 2 | 76 | 0.36 | 0.77 | 21 | empty |
| 3 | 73 | 0.33 | 0.75 | 18 | empty |
| 4 | 51 | 0.30 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 698 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 modified (disulfide, phosphorylation).
Compared structures
- 4KAY · Structure of the soluble domain of Lipooligosaccharide phosphoethanolamine transferase A… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q7DD94
- Elsewhere: RCSB PDB 4KAY · PDBe 4KAY · UniProt Q7DD94
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